{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA274378", "communityStandardTitle": [ "NM_138694.4(PKHD1):c.1830T>A (p.Tyr610Ter)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=186717[alleleid]", "alleleId": 186717, "preferredName": "NM_138694.4(PKHD1):c.1830T>A (p.Tyr610Ter)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/189100", "RCV": [ "RCV000169512", "RCV003152689" ], "variationId": 189100 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/6-51920391-A-T", "id": "6-51920391-A-T", "variant": "6:51920391 A / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr6:g.51920391A>T?assembly=hg19", "id": "chr6:g.51920391A>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr6:g.52055593A>T?assembly=hg38", "id": "chr6:g.52055593A>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/749293235", "rs": 749293235 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/6-51920391-A-T?dataset=gnomad_r2_1", "id": "6-51920391-A-T", "variant": "6:51920391 A / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/6-52055593-A-T?dataset=gnomad_r4", "id": "6-52055593-A-T", "variant": "6:52055593 A / T" } ] }, "genomicAlleles": [ { "chromosome": "6", "coordinates": [ { "allele": "T", "end": 52055593, "referenceAllele": "A", "start": 52055592 } ], "hgvs": [ "NC_000006.12:g.52055593A>T", "CM000668.2:g.52055593A>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000054" }, { "chromosome": "6", "coordinates": [ { "allele": "T", "end": 51920391, "referenceAllele": "A", "start": 51920390 } ], "hgvs": [ "NC_000006.11:g.51920391A>T", "CM000668.1:g.51920391A>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000030" }, { "chromosome": "6", "coordinates": [ { "allele": "T", "end": 52028350, "referenceAllele": "A", "start": 52028349 } ], "hgvs": [ "NC_000006.10:g.52028350A>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000006" }, { "coordinates": [ { "allele": "A", "end": 37033, "referenceAllele": "T", "start": 37032 } ], "hgvs": [ "NG_008753.1:g.37033T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001200" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 2094, "referenceAllele": "T", "start": 2093 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "ENST00000371117.8:c.1830T>A" ], "proteinEffect": { "hgvs": "ENSP00000360158.3:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS750727", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371117.8:c.1830T>A" }, "RefSeq": { "hgvs": "NM_138694.4:c.1830T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000360158.3:p.Tyr610Ter" }, "RefSeq": { "hgvs": "NP_619639.3:p.Tyr610Ter" } } } }, { "coordinates": [ { "allele": "A", "end": 2091, "referenceAllele": "T", "start": 2090 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "ENST00000340994.4:c.1830T>A" ], "proteinEffect": { "hgvs": "ENSP00000341097.4:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS261231" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "ENST00000371117.7:c.1830T>A" ], "proteinEffect": { "hgvs": "ENSP00000360158.3:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS268422" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "NM_138694.3:c.1830T>A" ], "proteinEffect": { "hgvs": "NP_619639.3:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS040823" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "NM_170724.2:c.1830T>A" ], "proteinEffect": { "hgvs": "NP_733842.2:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS042573" }, { "coordinates": [ { "allele": "A", "end": 1930, "referenceAllele": "T", "start": 1929 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514679.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512981.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081904" }, { "coordinates": [ { "allele": "A", "end": 1942, "referenceAllele": "T", "start": 1941 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514680.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512982.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081905" }, { "coordinates": [ { "allele": "A", "end": 2081, "referenceAllele": "T", "start": 2080 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514681.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512983.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081906" }, { "coordinates": [ { "allele": "A", "end": 2081, "referenceAllele": "T", "start": 2080 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514682.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512984.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081907" }, { "coordinates": [ { "allele": "A", "end": 2081, "referenceAllele": "T", "start": 2080 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514683.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512985.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081908" }, { "coordinates": [ { "allele": "A", "end": 1203, "referenceAllele": "T", "start": 1202 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514684.1:c.1119T>A" ], "proteinEffect": { "hgvs": "XP_011512986.1:p.Tyr373Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081909" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514685.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512987.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081910" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514686.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512988.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081911" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514687.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512989.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081912" }, { "coordinates": [ { "allele": "A", "end": 2081, "referenceAllele": "T", "start": 2080 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514688.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512990.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081913" }, { "coordinates": [ { "allele": "A", "end": 2081, "referenceAllele": "T", "start": 2080 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514689.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512991.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS081914" }, { "coordinates": [ { "allele": "A", "end": 2450, "referenceAllele": "T", "start": 2449 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514680.3:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512982.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543423" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514682.3:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512984.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543424" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514683.3:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512985.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543425" }, { "coordinates": [ { "allele": "A", "end": 1216, "referenceAllele": "T", "start": 1215 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514684.3:c.1119T>A" ], "proteinEffect": { "hgvs": "XP_011512986.1:p.Tyr373Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543426" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514686.2:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512988.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543427" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_011514688.2:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_011512990.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS543428" }, { "coordinates": [ { "allele": "A", "end": 1932, "referenceAllele": "T", "start": 1931 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010944.2:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866433.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564897" }, { "coordinates": [ { "allele": "A", "end": 1997, "referenceAllele": "T", "start": 1996 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010945.2:c.1755T>A" ], "proteinEffect": { "hgvs": "XP_016866434.1:p.Tyr585Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564898" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010946.2:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866435.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564899" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010947.2:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866436.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564900" }, { "coordinates": [ { "allele": "A", "end": 1890, "referenceAllele": "T", "start": 1889 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010948.2:c.1119T>A" ], "proteinEffect": { "hgvs": "XP_016866437.1:p.Tyr373Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564901" }, { "coordinates": [ { "allele": "A", "end": 1041, "referenceAllele": "T", "start": 1040 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010949.2:c.-59T>A" ], "proteinEffect": { "hgvs": "XP_016866438.1:n.-59T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS564902" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010950.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866439.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564903" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010951.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866440.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564904" }, { "coordinates": [ { "allele": "A", "end": 2072, "referenceAllele": "T", "start": 2071 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XM_017010952.1:c.1830T>A" ], "proteinEffect": { "hgvs": "XP_016866441.1:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS564905" }, { "coordinates": [ { "allele": "A", "end": 2106, "referenceAllele": "T", "start": 2105 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "XR_001743469.1:n.2106T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS592682" }, { "coordinates": [ { "allele": "A", "end": 2094, "referenceAllele": "T", "start": 2093 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "NM_138694.4:c.1830T>A" ], "proteinEffect": { "hgvs": "NP_619639.3:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS699767", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371117.8:c.1830T>A" }, "RefSeq": { "hgvs": "NM_138694.4:c.1830T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000360158.3:p.Tyr610Ter" }, "RefSeq": { "hgvs": "NP_619639.3:p.Tyr610Ter" } } } }, { "coordinates": [ { "allele": "A", "end": 2094, "referenceAllele": "T", "start": 2093 } ], "gene": "http://reg.genome.network/gene/GN009016", "geneNCBI_id": 5314, "geneSymbol": "PKHD1", "hgvs": [ "NM_170724.3:c.1830T>A" ], "proteinEffect": { "hgvs": "NP_733842.2:p.Tyr610Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS700451" } ], "type": "nucleotide" }